Micro-Electro-Mechanical Systems (MEMS) acoustic transducers are highly sophisticated devices with high sensing performance, small size, and low power consumption. To be applied in an implantable medical device, they require a customized packaging solution with a protecting shell, usually made from titanium (Ti), to fulfill biocompatibility and hermeticity requirements. To allow acoustic sound to be transferred between the surroundings and the hermetically sealed MEMS transducer, a compliant diaphragm element needs to be integrated into the protecting enclosure. In this paper, we present a novel fabrication technology for clamped micron-thick Ti diaphragms that can be applied on arbitrary 3D substrate geometry and hence directly integrated into the packaging structure. Stiffness measurements on various diaphragm samples illustrate that the technology enables a significant reduction of residual stress in the diaphragm developed during its deposition on a polymer sacrificial material.